Nancy's Poor, Poor, Gut!

I really enjoyed writing this piece, I think it helped a lot of people! 233 Comments if you care to go and read... -Tim

The American Food Project Rings in For a Commenter and Not Good (Why Resistant Starch Doesn’t Work for Some)

April 10, 2014 by Richard Nikoley 233 Comments

Tatertot Tim put this together for us, in collaboration with Dr. BG (Grace)

What's Lurking in your Guts? Potato Starch as Litmus Test for Gut Health

Earlier this week I was copied on an email from frequent FTA commenter Nancy, who had some important news. Her American Food Project results were in and she was a bit concerned:

Subj: Results from American Gut: my innards are quite f*cked up
Results attached with crude photography below.
For context, I was the one who responded the worst to the PS. Started it twice, about six months apart, and it led to nighttime and morning loose and urgent stools. It just wasn't working. Now we know why.
My population was/is PRET-Ty sucky. And Googling some of these geni and families is freaking me right out. The same family as the bacteria causing the plague? A bacteria extremely populous in me that is only supposed to be in whiteflies?? I'm a bit nauseous! This is like the opposite of Tatertot Tim's profile!

I took one glance at her AmGut report and could tell she was right, her innards were quite f*cked up.

 

 

Apparently when Nancy got these results, she started looking up names and discovered that some of these microbes were disease-causing and belonged in a whitefly. I did the same thing when I got my results, if you’ll remember: Resistant Starch: American Gut Project Real Results And Comparison (Very Big News).

The report also noted I had some rare types of microbes...

• Victivallaceae - A producer of acetate
• Limnobacter - A bacteria normally only found in high mountain glaciers, a tribute to my Arctic life, I suppose.
• And my favorite—because I am often thought to be a slacker—Slackia—a producer of a substance known as Equol.

[Editor's note: If Tim is a slacker, then I'm a reprobate derelict!]

With all these names readily searchable by anyone with one finger and an internet connection, it’s easy to get lost. Dave Asprey loved to tease that all my RS ingestion seemed to do for me was to insert rare gut bugs in my gut, completely ignoring the fact that I had virtually NO detectable pathogens: Is there such a thing as Bulletproof Resistant Starch?

In fact, “tatertot” who worked with Richard on this research, got his American Gut results back after lots of resistant starch. His biome was stellar, but it contained a lot of Limnobacter, a rare microbe normally found in glaciers. Who knows what’s going to eat the resistant starch you put in your mouth?

When I looked at Nancy’s report, a quick glance at the bar chart—with the massive area in keto-pee yellow—screamed at me. This is the bar we really don’t care to see. It's the bar that represents the Proteobacteria...the home of E. coli, salmonella, H. pylori, and cholera. Most people have a small band of these. But as you can see from the bars to the right of Nancy’s, most people have 5-10% of their sample represented by Proteobacteria. My sample showed I had about 2%.
So what's in this massive Proteobacteria band of Nancy’s? The charts show that one of her most abundant microbes is of the genus Morganella, at 25% of her total microbiome. But we're still missing a few specific microbes that comprise nearly 40% of her gut. ...So, I asked her to send me her full taxa report. From the full report, we can see that not only does Nancy have 25% Morganella, but also nearly 10% of an unnamed member of the Gammaproteobacteria Class, Enterobacteriaceae Family—which is precisely where E. coli lives. We don’t know for sure it’s The E coli; but at a minimum, we're talking relatives. Elsewhere on the report—in ranges of .02 - 2%—were no less than 24 other genera of Proteobacteria. For comparison, I had 12 genera. These are not all pathogens, and most are considered normal parts of the human gut. And, some Proteobacteria are actually good.
So, what’s the big deal? At tiny fractions, these bacteria are fine—everybody has them. A gut that has “broken bad,” however, favors the pathogens and allows them unimpeded growth and they then control the real estate. This is exactly what has happened in Nancy’s gut.
The genus Morganella has exactly one species—Morganella Morganii. M. Morganii, as it is more commonly called—that's en effing bastard of a microbe. But, it’s not that uncommon either—my report shows that I have approximately .01% of it. But it doesn’t take much Googling to find out that this is not who might want dominating your gut.
Morganella morganii is a facultative, gram-negative and anaerobic rod found in the feces and intestines of humans, dogs, and other mammals. It's known to be a causative organism of opportunistic infections in the respiratory tract, the urinary tract, and in wound infections. It can cause devastating infections in neonatal and postoperative stages—particularly in diabetic patients. The risk of infection is especially high when a patient becomes neutropenic as a result of myelosuppressive chemotherapy. Massive hemolysis can be associated with bacterial infection and has been reported mainly in cases of Clostridial or Vibrio sepsis.
But, it’s not all bad:
Morganella morganii is a species of gram-negative bacteria that has a commensal relationship within the intestinal tracts of mammals and reptiles, as normal flora. Although M. morganii has a wide distribution, it's considered an uncommon cause of community-acquired infection and it is most often encountered in postoperative and other nosocomial infections such as urinary tract infections.
Or is it?

M. morganii is motile via the use of a flagella. In some cases, it reacts to changes in the pH of the gut, as well as to changes in the state of the immune system. Since it's an opportunistic pathogen, it takes advantage of any compromise of the immune system—why it's most often detected  in hospitals after a serious injury or surgery, perhaps from its ability to hydrolyze and modify antibiotics through the presence of adhesins, and other enzymes.
When the host’s immune system is suppressed, M. morganii will rapidly invade the host and also cause specific IgA responses and as well as cause an increase in the volume of Peyer’s patches. It's also able to ferment sugar and is glucose positive.

So, it seems that in my haste to pimp prebiotics on an unsuspecting public, I told Nancy to go ahead and eat potato starch, one of M. morganii’s favorite foods.
When I’d realized what I’d done, I wanted to see what lame advice I gave this poor lady who, as I write this, is trembling and curled the fetal position as she awaits a call from the doctor to schedule an appointment—just kidding.
Our conversation on the blog went something like this, beginning early November, 2013:

Maybe someone can help me. I think I have a bad biome. I have been gluten free and focused on healthy animal proteins and fats including coco oil for three years. I am quite overweight because I am a chocolate junkie. I tried the RS about 4 months ago, starting with 1 tbsp in the AM and one at night, going up to 2 and 2. After a few weeks, my TMI became late at night, first thing in the morning diarrhea. So I attributed it to the RS and stopped. The D lasted for about 3 more weeks, then finally became more normal. Because it still lasted, I ended up concluding that the D was from some other reason.
This week, I decided to really clean up my diet, and get off the sugar, mostly quality milk chocolate but also sometimes too much fruit, or crème brûlée. I was urged to try the RS again because of it help keeping cravings down. For three days I did 1 tbsp morning and 1 before dinner. After day 2 the TMI was changing. And after day 3, the looseness was back, and the urgency. I stopped RS today because I just don’t have the time to sit home in the morning.
Does anyone know what is wrong with my biome? Obviously something is amiss. I haven’t had any antibiotics for maybe 5 years except what they give you during a c-section birth two years ago. I also get migraines from any probiotic pills, liquids, or vegetables (I love kimchi but it doesn’t love me). I drink 1 cup of commercial full fat plain kefir a day, and 1 bottle of commercial kombucha a night in hopes of fermentation.
I suffer about 8 migraines a month. Maybe there is a connection.

Here was her plea for help...would the FTA community come through? You decide:
Richard Nikoley says:

Nancy, darling. Your comment is palpable to me.
You are suffering, girl. And it’s far beyond any advice I can offer. My only suggestion would be to fix your diet first, by which I mean no sugar that’s not in real food, no grains. Real food only you go out and get yourself, prepare yourself with whatever natural fats are your preference. Maybe feel free to include some of the foods touted for RS, but you probably ought stop supplementing it until you’re healthy.
You might consider seeking out pro help in the Real Food realm.

Then a nice number of helpful folks showed up, as is pretty common, here:

• Nancy, based on what I know (but I could be wrong), RS works really well for gut dysbiosis, i.e., dysbiosis in the large intestine. It may not be that effective for SIBO or IBS.
• I always crave chocolate. I find if I eat liver the cravings go away!
• ...for what it is worth, what I found what worked for me a while back was raw, natural, unprocessed honey

Then, thank doG, Ellen came along:

Ellen says:
Nancy,
WARNING serious tmi ahead.
When you say that the PS makes you go more often, is it actual watery D or a well formed stool that is just frequent with cramping?
I was having the latter (plus headache) from more than a tiny bit of either PS or foods high on RS and have been taking Prescript-Assist for several days and it seems to be changing things for the better.
But, either way, I don’t think it can do you any harm to try a top quality probiotic.
The bottom line however is that nothing is going to change if you don’t get off the sugar. I would suggest that the higher carb end of PHD style eating might help you avoid the sugar cravings.

I had to have a say, too:

Tatertot says:
Nancy – I concur with everybody else! You would probably be wise to look for a naturopathic doctor and get this all straightened out. Right now you are shooting in the dark, something is going on, you owe it to yourself to get it fixed.
Don’t bother with the American Gut Project unless you just want to give them money. They take 6+months to get back with you and only identify gut microbes to the family level–not species level. Here is a better place.
This is a full report and quicker for not much more money. I have a buddy who can help you interpret the results if you need explaining, just post back here and we’ll get it figured out.
In the mean-time, green bananas have been used forever as a treatment for diarrhea in 3rd World Countries. I’d highly recommend buying a bunch of the greenest bananas you can find and eating 1-3 daily. If they are too hard to peel, slice them in half lengthwise and peel sideways. They taste like crap when that green, but eat while drinking hot tea or coffee to wash them down.
Oh, and quit eating milk chocolate! Learn to eat 100% Baking Chocolate, or buy the 90-100% candy chocolate. There is no high-quality milk chocolate!

Then Richard Nikoley says:

Nancy:
Please go also post your comment at my long time friend Dr. BG’s blog, Animal Pharm.
She can probably help.

So, you all decide: were we helpful or hurtful in this situation? I think we all handled it pretty well. It turns out that, back in November, Nancy had just sent off a sample of her poo to the American Food Project and decided she’d wait to see the results—returning to her diet that she knew would keep her in the most comfortable range of gastric disturbance, a low-carb paleo approach.
Also, in related emails, I dug a bit into Nancy’s background. She’s led quite a hectic life and her gut bugs have taken the brunt of the punishment. Many rounds of antibiotics, a benign brain tumor (prolactinoma on pituitary) removed—and grown back, and the usual array of health issues surrounding most everyone. She’s hypothyroid, and has frequent migraines. She’s Mom to 4 active children.
Would any of this info have swayed our musings? Probably not. So, what lessons can we learn from Nancy...amazing Mom who was overweight and had some TMI troubles, looking to resistant starch and a bunch of internet morons to help her out, i.e., just cut the carbs?
I think the big lesson we need to take from all this is that if potato starch f*cks you up, you need to go to a doctor ASAP. Get a full gut health report. Eating in a way that alleviates symptoms is not the same as eating in a way that is helping you out...it may just be doing the exact opposite! How many thousands of people get operated on every day in this same condition? Do doctors and surgeons routinely check for this kind of thing? Doubtful. It’s entirely possible that Nancy’s life will now improve, now that eating cheap Bob's Red Mill Potato Starch, 24-Ounce (Pack of 4) identified a clear gut problem. For many months, we have heard loud and clear from those who conclude it's not about them that they can't handle it, when the clear evidence is that better than 90% of people can.
Here's someone who took the time and trouble to find out.
...Another lesson is that if you think you have gut troubles, don’t mess around with the American Gut Project. Get a real test, like the Metametrix GI Effects stool analysis and get a urine test while you're at it. These will need a doctor’s help and prescription, involving insurance paperwork and all that, but it may end up really improving your life. The American Gut Project is wonderful, but only for basic amusement. It only shows the level of diversity you have in your guts—which is totally fascinating—but potentially misleading. It won’t show yeasts, or put up a red flag if something is seriously amiss. Had Nancy not thought to share her results, she might have just gone on her merry way thinking that 25% Morganella was perfectly acceptable. Nancy may also find she has even more sinister inhabitants when examined fully.
...The gut is an amazing piece of machinery. Your gut microbes can exert a form of mind-control and do it all the time. This M. morganii, for instance, that has taken over Nancy’s prime neighborhoods, loves to eat sugar. What was Nancy admittedly addicted to? Sugar. M. morganii should also be able to eat RS as it is a form of carbohydrate, but it’s almost as if Mr. Morganii didn’t want her to have it—because it would also feed his enemies...and...diarrhea for weeks!
Nancy suffers migraines, why do I have a strange feeling that these are related to her gut? Are these migraines the remaining few good gut bugs screaming for help? Or M. morganii hoping she’ll seek solace and comfort in a piece of apple pie?
What advice would Nancy have gotten from any of the other gastrointestinal ‘gurus’ out there? Hopefully, they would have first advised her to get a full report. We are beginning to see, now, that the information you can get from genetically sequencing your poop can add up to gold.
Nancy further relates, within the last few day, and a few months later:

I started taking Prescript-Assist Probiotic 6 weeks ago. With one a day, taken at night before bed. Within 48 hours my poop and my life changed for the better. Instead of quite urgent but controllable poop that was not on the Bristol scale (I liked to call it ‘sludge’), I went to shaped poop that kept the shape even in the bowl. On the Bristol scale and one of the good ones, I think. And if someone is in the bathroom, I can wait my turn. This was a change I welcomed.

As to Resistant Starch and her diet lately:

I only eat RS in the form of cooled rice really, right now. I was planning to start Potato Starch soon, now that my stools are changed and maybe my biome too? I have to go very easy with most fermented foods, like kimchi or real sauerkraut. Love them, but more than a tablespoon and I get a migraine. I drink a cup of commercial plain full fat kefir maybe 3-4x a week. I drink half to one bottle of chia kombucha a night. That is as much alcohol as I can handle without migraine. It's the weak kind of kombucha that you can buy under 21.”

Hopefully, when Nancy gets her gut bugs re-checked very soon, she’ll find that the Prescript-Assist, fermented foods, and rice have turned the tide and her gut is well on the way to healthy.
Some advice from Dr. BG on what tests to ask for can be found on her blog.
Grace’s thoughts on RS failures are that there are four main reasons why people can have a hard time when they first start an RS rich diet:

1. SIBO/SIFO—Small Intestine Bacterial or Fungal Overgrowths. RS utilizing bugs in the wrong place (right bugs, wrong place). The only way to tell is with testing.
2. Antibiotics have removed the RS utilizing bugs—over 25% of individuals make zero butyrate with RS due to missing ‘core’ gut bugs.
3. Parasites, yeasts and pathogenic strains in the small intestines and/or colon—either too much (or too little) butyrate, propionate, or acetate production depending on which strains, how much and where in the enormous ecosystem.
4. VLC or ‘Atkins’ type diets—drops butyrate to 1/4 of control diet. Symbiont RS-utilizing strains are decimated analogously, particularly Roseburia which tracks with butyrate production.

So if you think you have a serious problem in your gut, please don’t mess around—get it checked out. Maybe it's not the potato starch. Maybe it's you. Spend some money and get a real test done. Waiting 6 months for an American Gut report is fine if you're generally healthy; but if you cannot eat real food, like potato starch or cold potatoes—you just may be ill, from the perspective of a normal human. Resistant starch is an age-old food, one we evolved millions of years eating. If you can’t eat it, you probably need some modern medicine to find out why. Hopefully, Nancy will get her appointment and a new stool test very soon and she and her doctors will come up with a solution to restore balance and heal her gut fully. Last word is, she's well underway with that.
What’s lurking in your guts?
~~~
Editor's comments: Let me close with a little hubristic spice. It's not a question, anymore, about all the millions of folks who've invested countless dollars and time in oder to fully understand every metabolic pathway, every axis, or every single genetic expression that they just love to go on and on about.
None of it—regardless of how detailed and precise—has even a sliver to do with a scintilla of all of the foregoing. What does that mean? Smart people, but smart people who are literally back at the drawing board. Every one of them. And I'm talking day one, and kindergarten—and I care not their names or credentials. Meaningless.

1. When they are talking about metabolic function, hormonal signaling, et al, they are talking, at most, about 10% of you. Until they fully integrate the gut biome's role in all of this and minimally, begin to start classifying different levels of healthy guts vs. bad guts, they ought be regarded as going bla bla bla.
2. When they are talking about gene expression it's even worse, and more embarrassing, since our own genome is less than 1% of the total genome including the up-to 1,000 lines of microbiota.

I'll tell you what's far more hubristic, though; and I'm just alerting you, because you're going to see it a lot—from those who invested so much to be "experts" on 10% and 1%. It's very simple and you watch. You are going to see tons of people who are behind, who thought they were the Bee's Knee's tell you it's all a bunch of BS, don't look. Watch for being told not to look.
That's exactly how things shift from who knows nothing, to who knows everything—and vice versa—in every paradigm shift; and if the science of the gut microbiota doesn't represent a back-to-the-drawing-board paradigm shift in health and medicine, then nothing does.
Stay tuned for the book. The foregoing represents a Tim drafted, but Richard and Grace collaboration—with me as your final say editor. Hope you liked it.